Bora recently asked whether anyone was using Connotea. I am, and I like it fine. It’s open source and has a web API, there’s a lively dev forum, and it’s continually improving. You could use any bookmarking service, like Simpy, to collect your science/work-related links, of course, but Connotea offers the compelling advantages of auto-discovery of relevant fields (DOI, author list and so on), an improving ability to play nice with reference manager software, and a more focused community with whom to share tags, bookmarks and ideas.
Now, much to my glee, Connotea has started actively supporting citations to blog entries:

A lot of you are increasingly bookmarking articles from personal blogs alongside traditional journal-published articles. In response to this, Connotea now has experimental support for treating bookmarked blog posts as citations, and it will automatically import publication data for those articles wherever possible.

Hot damn, says I! Of course I had to try it out, on the obvious test post. Here’s a screenshot, with a regular PubMed entry for comparison:

As you can see, Connotea correctly identified the blog, although it didn’t grab the entry title (and I’m not the only one reading Science & Politics!).
This is the sort of thing that makes me feel that there really is an open science revolution underway. The internet is making possible real-time collaboration between large numbers of people with minimal regard to geography; as proprietary barriers to information flow are dismantled, this collaborative process can only accelerate and will, I believe, supplant traditional competitive models of research.


hybridbear.jpg The headline says “DNA Tests Confirm Bear Was a Hybrid” (see also here). “Was”, as in, this is an ex-bear. It was a naturally occurring interspecies hybrid; now it’s a corpse, since some dickless macho yuppie fuckbag stood off a safe distance with a high powered rifle and a telescopic sight and killed it, presumably because wasteful slaughter is a soothing salve for the inflammation of the ego that comes with being a sniveling coward who wants so very badly to be a tough guy.
I hope “hunter” Jim Martell (left, in the chic white parka) dies of explosive rectal prolapse. I hope it happens on his very next “hunting” trip, and I hope he is still conscious when whatever he was “hunting” wanders over and starts gnawing on his guts.

Fucking bastards.

From hilzoy, a snapshot of just how desperate the armed forces have become for fresh meat to feed into their pointless fucking grinder:

Jared Guinther is 18. Tall and lanky, he will graduate from high school in June. Girls think he’s cute, until they try to talk to him and he stammers or just stands there — silent.
Diagnosed with autism at age 3, Jared is polite but won’t talk to people unless they address him first. It’s hard for him to make friends. He lives in his own private world.
Jared didn’t know there was a war raging in Iraq until his parents told him last fall — shortly after a military recruiter stopped him outside a Portland strip mall and complimented his black Converse All-Stars.
“When Jared first started talking about joining the Army, I thought, `Well, that isn’t going to happen,”‘ said Paul Guinther, Jared’s father. “I told my wife not to worry about it. They’re not going to take anybody in the service who’s autistic.”
But they did. Last month, Jared came home with papers showing that he had not only enlisted, but signed up for the Army’s most dangerous job: cavalry scout. He is scheduled to leave for basic training Aug. 16.

Fuuuuuuuuuuuuuuuuuck. Turns out the parents got the media involved and there’s an investigation underway; see the linked stories for details. I guess Jared won’t die in Iraq after all, but not for lack of trying on the part of the recruitment vultures.
(I’m somewhat angry at myself, too, for a missed opportunity. I was recently a judge at the Northwest Science Expo, a local science fair for middle and high school students and part of the Intel International Science and Engineering Fair. ( It was a blast, and I encourage anyone who’s interested to get involved; that’s not my point here though.) There were a handful of broomstick-up-my-ass types wandering around in medal-bespangled uniforms, because in addition to the usual awards there are various military scholarships and prizes available at these fairs. Next time, I’m going to turn up in a t-shirt reading “hired killers off our campuses” or something like that.)

New to the blogroll.

Dr Free-Ride linked to Zuska (Goddess of Science, Empress of Engineering, and Avenging Angel of Angry Women) talking about sexual harassment in science, in light of a recent study linking a sense of injustice among researchers to the probability that they will compromise their integrity. Zuska’s Seven Scientific Commandments, paraphrased, are:

  1. Do not rape your students and colleagues. No means no. Coercion is rape.
  2. Don’t engage in sexual harassment, either. If you don’t know what that is, your university will have policies in place and people willing to explain them.
  3. Er, that all goes for grad students too.
  4. The points above all apply “even if you think she’s willing or she wants it or she’s asking for it or she needs it or whatever other excuse you come up with to put the agency on her and absolve yourself of guilt. They also apply even if she is actually willing.”
  5. Racial harassment? Also a no-no.
  6. Don’t steal ideas.
  7. Don’t steal ideas that have been published (that’s plagiarism).

There’s more to each point, including links, so do read the whole thing. Me, I continue to be astonished by my own naivete. I was aware that sexual harassment is a problem in science — I’ve seen a few instances, and I’m even aware that I only saw most of those instances because the women involved stood up for themselves. But rape? Yes, rape. Zuska is serious. I am — horrified.
Zuska, in turn, led me to Dr Shellie, who describes her blog as

…a year-long project to develop and articulate my opinions on the following themes, as they apply to my life and research:

  • women in science
  • how to improve the culture of science, particularly in academia
  • societal benefits of science and technology

There’s plenty to read in the couple of months Dr Shellie’s been blogging, but just to continue the theme of this post for a moment, here’s (part of) her take on women in science:

Making science departments more welcoming to women and minorities will result in a better working environment for everyone. Fortunately, a number of great initiatives are in place to do just this. Some of the main issues are to:

  • Insure equal recognition for equal work.
  • Encourage all students to actively participate in classroom activities in research, particularly talented students with low initial confidence.
  • Value scientific contributions and content, not aggressiveness and self-confidence. Teach scientific communication skills and conflict resolution techniques.
  • Promote role models for women and minorities in science and engineering.
  • Work to accommodate dual-career issues and hiring concerns, which disproportionately affect women scientists.
  • Develop university policies to accommodate childbirth and parental child-care responsibilities.

Again, there’s more to each point than I’m copying here, including a good many links to resources and references, so go read the original post. I just want to focus for a moment on the first three points. There’s nothing in those that is necessarily specific to women; that they apply more to women than men is a reflection of the general social disadvantage that affects women. Momentarily taking sex out of the language makes it clear that we are talking about a rising tide that will lift all boats: male and female scientists alike will benefit from changes in the culture of science that focus on rewarding merit and promoting cooperation. This is much the same as my usual “bottom line” argument in support of feminism: placing half of the population at a systematic disadvantage is a waste of human resources and a net loss for the population as a whole. Conversely, equality of opportunity across all demographics allows for the most efficient possible use of those human resources. It’s clear that my interest in open science

Anything to do with open access to source code, published information, raw data, &c. Blogs, wikis, databases, journals, anything that views information and information sharing as common goods or could be used to further that view. Also anything to put collaboration ahead of competition.

— has much in common with the interests and goals of feminist scientists.

linklog 060509

  • Uncommon Places
    From Dana Doyle’s review:

    In the late 1960’s William Eggleston subverted photographic tradition by embracing color film and irregular compositions reminiscent of snapshots. The prints I have seen by Eggleston (which include many of his iconic images now traveling in an exhibit titled “Los Alamos”), lose their resolution when you get within a few feet.2 The fuzziness of the print echoes the implication of amateur work already knowingly signified, at the time, by color film and the snapshot aesthetic. Shore’s prints, less than half the size of Eggleston’s, are meticulously crisp in comparison. In his Uncommon Places, Shore tweaks Eggleston’s subversion: he similarly embraces color film and vernacular subject matter, however he brings the full arsenal of traditional photographic craft to bear on what was popularly considered unworthy subject matter for the art photographer.

    There’s more than nostalgia to Shore’s photos; it’s not just that he’s taking photos that you (feel you) could have taken. Look at “Merced River”, for instance: is that not every afternoon anyone ever spent by any river? The very ordinariness of the scenes combines with the high-quality images and sneaky formal underpinnings of the compositions to create both immediacy and timelessness. Or something. This shit is hard to write about.

  • | SPARC | SPARC Resources |
    Yet another “I have no excuse” link: SPARC has collected everything I need to start writing about open access.
  • Airline Pilot Central – FedEx arrivals during Thunderstorms
    I like the way the little dots — they’re planes, but I was thinking of ants with a parasol in one hand and a package under the other arm — make their way around the storm, then scatter to all points when it finally hits the airport. It’s actually a very impressive demonstration of what air traffic controllers do. (Hi, John!)
  • american atheist or agnostic | Ask MetaFilter
    This is something AskMeFi is really good at — lots of little windows into other people’s lives. In this case, do atheists/agnostics in the US feel discriminated against?
  • Bitch Ph.D.: The Hooker Resurgence
    My ancestors were fishermen. Fishermen, damn you. But I do like “prostiboots” and especially “Fornigate”.
  • Surname Profiler
    It appears that my surname arose in London sometime before 1880. Or, you know, maybe not. But this thing is kinda fun.
  • Cole/Weisberg Correspondence on Hitchens
    Jacob Weisberg: “In my judgment, there is no ethical issue here.” Note to self: never trust anything published in Slate.
  • How Opal Got Openly Despised / Take perverse joy in the downfall of that plagiarist teen author? Can you flip that upside down?
    Once again, Mark Morford is right; his is the best take I’ve seen on the Viswanathan incident, bar none: “Deserved or not, Viswanathan’s success and even her stunning failure are excellent motivators by which to pinch and flip around and strip naked your relationship to accomplishment. Is it all about envy and bitter Schadenfreude, or exultation and lessons learned? From where do you draw your sustenance?”
  • Open Access News
    Nature has released the API for Connotea. Sooner or later, I’m gonna have to learn to program for the web.
  • Being a mom could be a 6-figure job
    I usually think overinflates everything, but these don’t look much inflated to me. “ determined that a stay-at-home mother might be paid as much as $134,121 for her contributions as a housekeeper, cook, day care center teacher, janitor and CEO, among other functions. (See full list at right.) The stay-at-home mothers surveyed said they logged a total of 92 hours a week performing those jobs. The market valuation for working mothers — who make up close to 70 percent of all mothers with kids under 18 — comes to $85,876, assuming a 50-hour week in the Mom role. That would be on top of whatever salary a working mother draws from her job outside the home, working 44 hours.”
  • Isaac Laquedem: Endorsements I: Ted Wheeler and Lonnie Roberts
    Lonnie Roberts is a homophobic scumbag, and I wouldn’t write him in as a candidate to shovel shit.
    Neat idea: “We will produce a series of 1000 unique postcards, each depicting a single unpublished image from a relatively unknown designer, and we will send them to a selected group of 1000 influential architects, urbanists, academics, curators, journalists, and critics, who will have the opportunity to respond. Our hope is that we will receive images from all over the world and our plan is to randomly disseminate these images back out into a global context, making unlikely connections, and creating unforeseen acquaintanceships. While this is admittedly a utopian proposal, our aim is to connect fresh ideas with those individuals who contribute to the development of independent careers in architecture. ”

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Bora could use a hand.

I talk a lot about community — the blog community, the local community, the community of science. I think of “community” as a way to help create, and to be part of, something larger than oneself, something capable of more than one could achieve alone. I suppose, though, it’s equally valid to see it as a kind of insurance: by contributing to the maintenance of a network of trust and mutual assistance, we assure our own access to assistance when we need it. Either way, a community is, among other important things, a means of spreading risks and costs so that no single incident should be catastrophic to any given individual.
Which is why it is exceeding remiss of me not yet to have mentioned that Bora could use a hand. He’s a grad student with a thesis in the balance and a family to help support, and the bills have piled up enough to be a hassle right now. As Abel Pharmboy says in comments there,

This is nuts […] but sadly all too common among the academic world these days. [Bora] should have a tenure-track position at a major scientific or liberal arts university but [is] stuck in the cycle of teaching-on-demand for far less than [he deserves].

More to my point, Bora’s a member of my community: inter alia, a researcher and a science blogger. And if you happen to be a blogger, teacher and/or researcher, consider this: Bora is the sort of person we want in our community. It will not take much reading of his main site, or his associated teaching and research blogs (Magic School Bus and Circadiana, respectively), to convince you that he has talent for science and for science teaching; nor will it take more than a glance at the support he has given various blogging carnivals to demonstrate that he understands and values community; nor is it necessary to look beyond his writing about science blogging itself to see that he has a forward-looking, can-do way of thinking about science and community and what the two can do for each other.
So: Abel and I have sent a little beer money Bora’s way, and now I’m asking my readers to do the same if they possibly can (PayPal and Amazon links are on the right hand side on Bora’s site). Please also consider passing on the request if you have a blog of your own.

Nurses’ Day

Orac points out that today is National Nurses’ Day in the USA. In fact, National Nurses’ Week runs from May 6-12, and International Nurses’ Day is May 12 — Florence Nightingale’s birthday. The romantic myth largely obscures the real story when it comes to Florence Nightingale, and it’s all too easy to fall into that view of nurses and nursing: the ministering angels, all heavenly compassion and hot towels. The problem with this view is that it plays up the comforting hand on the brow at the expense of the highly trained hand clearing the intestinal blockage. Orac exhorts patients to “show how much you appreciate their caring work”. Because “caring”, see, the fluffy bunny stuff, that’s what nurses do — they hold hands and wipe arses. The real work is done by doctors, of course.
To be fair, I’m pretty sure that’s not what Orac meant. But given that this patronising view of nursing is all too common, it’s what he said. (Or, because this is something of a hot-button issue for me, it’s what I heard.)
So anyway, happy Day to any nurses reading, and my personal thanks to you and your profession for all the misery you’ve saved me from over the years.

linklog 060503

  • The Priory Of Sion – CBS News
    “”I am not a naive innocent who was hoaxed by Monsieur Plantard and Cherisey. No, I am a very, very careful researcher,” says Lincoln. ” Bwahahahaha!
  • Informed Comment
    Hoo boy, Juan Cole is pissed. I sent Slate this:

    Dear Slate, if you want to retain a shred of credibility, you must provide Prof Juan Cole with a forum in which he can reply directly to Christopher Hitchens’ ill-considered and underhanded attack on him (see here).
    I understand (from Prof Cole, among others) that Hitchens was once a fine journalist. However true that may be, and however laudable may be your loyalty to him, with this latest attack Hitchens has crossed a line that no reputable publication dare cross with him.

  • Great Plant Picks
    “Great Plant Picks is an educational awards program committed to building a comprehensive palette of outstanding plants for Pacific Northwest gardens. Awards are based on the combined expertise of over forty horticulturists from Washington, Oregon and British Columbia. Great Plant Picks originates at the Elisabeth Carey Miller Botanical Garden in Seattle, Washington, and provides a forum for sharing horticultural information with the wider gardening community.”
  • The Common Cold – The Scientific Indian
    Selba has a code doo.
  • Flags and Lollipops – Bioinformatics Blog: Commenting on papers
    BioMedCentral has a comments page for each paper, Nature has a blog, and now Cell has comments for selected papers as well. Eee!
  • Digby’s right, we should just flat-out buy them. Cheaper by the dozen I bet.
    “Since I see little hope that the system is going to be reformed, it occurs to me that we liberals should just hire ourselves some lobbyists. Really. We spend many, many millions on political campaigns that get us zilch. Nada. We should just raise funds to buy congressmen yachts or send them to Australia on vacation or hire their wives at 5 grand a month to survey what congressmen like for dinner. These guys go cheap when you really think about it. They’ll do pretty much anything you want for a golfing trip. We’d actually save money just by buying them all French commodes. In exchange we get them to vote for national health care and legal gay marriage and a $15.00 minimum wage. “
  • :: Sudan Research, Analysis, and Advocacy
    Darfur. Horrible.
  • So what can I do?: Make trade fair.
    From Karama Neal’s excellent blog, a list of fair trade clearinghouses that enable the consumer to make informed ethical choices.
  • | Society Guardian | Hard to swallow
    Researchers at the University of Chicago have calculated the relative carbon intensity of a standard vegan diet in comparison to a US-style carnivorous diet, all the way through from production to processing to distribution to cooking and consumption. An average burger man (that is, not the outsize variety) emits the equivalent of 1.5 tonnes more CO2 every year than the standard vegan. By comparison, were you to trade in your conventional gas-guzzler for a state of the art Prius hybrid, your CO2 savings would amount to little more than one tonne per year.
  • Women’s Bioethics Blog
    I figure we should include science/bioethics blogs in any list of “science blogs”.
  • ResourceShelf
    Society and Religion–Resource Round-Up
  • Plushy Bugs!
    We make stuffed animals that look like tiny microbes—only a million times actual size! Now available: The Common Cold, The Flu, Sore Throat, Stomach Ache, Cough, Ear Ache, Bad Breath, Kissing Disease, Athlete’s Foot, Ulcer, Martian Life, Beer & Bread, Black Death, Ebola, Flesh Eating, Sleeping Sickness, Dust Mite, Bed Bug, and Bookworm (and in our Professional line: H.I.V. and Hepatitis).

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linklog 060501

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